Information

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Antimicrobial Resistance Report: Outbreak

REPORT DATE OUTBREAK ID PROJECT NAME PREPARED BY
20250303 test test S. Chill

METHODS

The figures shown here were generated using sequence data processed with the ODH AR data analysis pipeline. If you have questions about this report please contact Samantha Chill. The following databases are utilized to generate the data within this report:

  1. AMRFinderPlus database: Version 2023-04-17.1

  2. ARG-ANNOT database: Latest version NT v6 July 2019

  3. ResFinder database: v2.1.0 including until 2023-04-12 commit f46d8fc

  4. MLST database: static db generated from PubMLST.org 2023-05-02

  5. Kraken database: standard-8 db

Phylogenetic trees visualize the relatedness and genetic diversity of samples. Closely related samples will generally share a recent common ancestor. Three different types of trees are presented.

Core Genes Identified: 30

Total Genes Identified: 11684

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Summary

There were 4 samples analyzed and 2 samples passed quality control thresholds, while 2 failed. Failing samples included: ODHL_sample1 | ODHL_sample3. An additional 3 samples were used for reference (ODHL_ref, REF).

DISCLAIMER

The information included in this report should only be used to support infection prevention measures. This report should not be used to guide treatment decisions, nor should it be included in the patient record. Whole-genome sequencing analysis is a rapidly evolving technology. Whole-genome sequencing and single nucleotide variant analysis will continue to be adjusted and refined over time due to the varied nature of bacterial genomes, limitations on available reference genomes and continual assessment of the inclusion of mobile genetic elements in this analysis. These results represent the most advanced method currently available for genome comparisons.

Analysis

Phylogenetic Tree

Ancestrial Tree

A phylogeny tree is used to illustrate relationships where a simulation of continuous trait evolution is illustrated (Brownian motion BM model). The “trait value” refers to the values of the simulated continuous trait for each tip (or node). The length of each branch is representative of lineage relatedness.

Cladogram

A cladogram is used to illustrate relationships, where nodes are labeled with degree of similarity, but where the vertical lines are not representative of lineage relatedness.